Despite two delays, council president Muhammad Bahr al-Ulum and the 25 other members came up one by one to put their signatures to the document on Monday.
Applauded by a gathering which included US occupation administrator Paul Bremer, Shia and Kurdish representatives signed the constitution after some hard negotiating the previous week.
Shia council members announced on Sunday that Grand Ayat Allah Ali al-Sistani still had deep reservations about the document but had given them the go-ahead to sign in the interests of advancing political transition.
Under a US timetable, an Iraqi government is to take over sovereignty on 30 June and elections for a transitional assembly are to be held by the end of January next year.
Another point of dispute had been a clause in the constitution that might allow Iraq's Kurdish minority to veto a planned permanent constitution should it not enshrine their right to autonomy in three northern provinces.
The Kurds, who have ruled three provinces of northern Iraq since wresting them from Saddam Hussein's control after the 1991 Gulf War, had said that if the clause was not included they would not sign.
Twice last week it seemed no
interim agreement would be signed
The issue risked opening a new rift among Iraq's ethnic and religious groups.
Bremer denied the unresolved issues represented a setback to the process of restoring self-rule to Iraq a year after US-led forces invaded to topple Saddam Hussein.
"What we are seeing here is a perhaps confused and perhaps initial way in which democracy works," he said. "This is kind of normal democratic habits working themselves out."
But the Shia dispute illustrated the influence that the 73-year-old Ayat Allah al-Sistani holds over the political process.
The interim constitution had been agreed unanimously by the council at the beginning of last week.
But with the Ayat Allah opposing the deal, five out of 13 Shia members refused to sign only hours before the first planned ceremony was to take place, breaking unity on the body and embarrassing US officials.